mass spectrum of hexane fragmentation pattern of m/z m/e ions for analysis and identification of hexane image diagram doc brown's advanced organic chemistry revision notes

Advanced Organic Chemistry: Mass spectrum of hexane CH₃(CH₂)₄CH₃

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Interpreting and explaining the mass spectrum of hexane CH₃(CH₂)₄CH₃

[Author © Dr Phil Brown PhD: Doc Brown's advanced level organic chemistry exam revision notes suitable for students of UK A level chemistry courses, IB chemistry & US K12 grade 11, grade 12 and AP honors chemistry courses: Molecular spectrometry analysis of hexane [spectrum page updated Mar 24th 2026 *]

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Mass spectrometry - spectra index

and details of the Isomers of molecular formula C₆H₁₄ (M_r = 86)

Introductory note on the mass spectrum of hexane

Students and teachers please note my explanation of the mass spectrum of hexane is designed for advanced, but pre-university, chemistry courses.

If M represents the hexane molecule, the initial ionisation to give the molecular ion is:

M_(g) + high KE e^- ==> [M•]⁺_(g) + 2e^- and for fragmentation equations assume [M]⁺ is the start of the processes and all species are in a gaseous state.

I've not usually shown an unpaired electron on e.g. an ion or a non-ionised alkyl radical R e.g.

[M•]⁺ ==> [X]⁺ + R•, but you should be aware this is a more accurate depiction of some processes.

I've used simplified equations to show how some of the ions that might be formed in the fragmentation pattern for the mass spectrum of hexane and only the formation of singly charged positive are considered for the mass spectrum of hexane.

I've included a stick diagram and table of m/z ions for the mass spectrum of hexane and doing the mass spectrum analysis under standard conditions, databases can be compiled based on complex fingerprint patterns, often involving the relative intensities of many fragment ions, and used to identify compounds including hexane.

In selected cases, where two different fragment ions have the same integer m/z value, I've pointed out that modern mass spectrometers can measure relative ion mass to four decimal places. So, using accurate isotopic masses, I've calculated the accurate ion masses, BUT strictly speaking, 0.0005 should be deducted for singly charged ions to account for the loss of the electron in their formation. I have NOT done this for hexane, but the mass spectrometer software does!

mass spectrum of hexane fragmentation pattern of m/z m/e ions for analysis and identification of hexane image diagram doc brown's advanced organic chemistry revision notes

Hexane C₆H₁₄, , ,

an alkane For more see The molecular structure, classification and naming of alkanes

Interpreting the fragmentation pattern of the mass spectrum of hexane

[M]⁺ is the molecular ion peak (M) with an m/z of 86 corresponding to [C₆H₁₄]⁺, the original hexane molecule minus an electron, [CH₃CH₂CH₂CH₂CH₂CH₃]⁺.

The small M+1 peak at m/z 87, corresponds to an ionised hexane molecule with one ¹³C atom in it i.e. an ionised hexane molecule of formula ¹³C¹²C₅H₁₄

Carbon-13 only accounts for ~1% of all carbon atoms (¹²C ~99%), but the more carbon atoms in the molecule, the greater the probability of observing this ¹³C M+1 peak.

Hexane has 6 carbon atoms, so on average, ~1 in 17 molecules of will contain a ¹³C atom.

A similar argument applies to fragment ions from the breakdown of the parent molecular ion of hexane - though the ratio will be greater e.g. the m/z 58 ion.

Identifying the species giving the most prominent peaks (apart from M) in the fragmentation pattern of hexane.

The most abundant ion of the molecule under mass spectrometry investigation is usually given an arbitrary abundance value of 100, called the base ion peak, and all other abundances ('intensities') are measured against it.

Base ion peak for the mass spectrum of hexane is the m/z 57 ion [C₄H₉]⁺ or [CH₃CH₂CH₂CH₂]⁺

m/z value of [fragment]⁺	71	58	57 [C₄H₉]⁺	56	55
[molecular fragment]⁺	[CH₃CH₂CH₂CH₂CH₂]⁺	[¹³C¹²CH₁₀]⁺	[CH₃CH₂CH₂CH₂]⁺	[C₄H₈]⁺	[C₄H₇]⁺

m/z value of [fragment]⁺	43	42	41	39	29	28	27
[molecular fragment]⁺	[CH₃CH₂CH₂]⁺	[C₃H₆]⁺	[C₃H₅]⁺	[C₃H₃]⁺	[CH₃CH₂]⁺	[C₂H₄]⁺	[C₂H₃]⁺

Analysing and explaining the principal ions in the fragmentation pattern of the mass spectrum of hexane

PLEASE NOTE I have found it difficult to find 'authentic' equations to explain mass spectra fragmentation patterns and it is complex chemistry! I've identified the formulae of the ionised fragments on the mass spectrum diagram, but the equations are from the internet or my conjecture as to how the ions might be formed - please take care in using the information, especially for assignments at university or pre-university level.

Atomic masses: H = 1; C = 12 (13 for ~1 in 100)

Bond enthalpies = kJ/mol: C-C = 348; C-H = 412

Examples of possible equations to explain some of the most abundant ion peaks in the mass spectrum of 2-methylpentane

Formation of m/z 71 ion:

[CH₃CH₂CH₂CH₂CH₂CH₃]⁺ ===> [CH₃CH₂CH₂CH₂CH₂]⁺ + CH₃

C-C bond scission in the carbon chain of the molecular ion of hexane giving a [C₅H₁₁]⁺ ion, cleavage releasing a methyl group.

Mass change: 86 - 15 = 71 (M-15 ion peak)

Formation of m/z 57 ion:

(i) [CH₃CH₂CH₂CH₂CH₂CH₃]⁺ ===> [CH₃CH₂CH₂CH₂]⁺ + CH₂CH₃

The m/z 57 ion is the base peak ion, the most abundant and 'stable' ion fragment.

Again, C-C bond scission in the carbon chain of the molecular ion of hexane.

Loss of ethyl group, mass change = 86 - 29 = 57 (M-29 ion peak)

Similarly the m/z 57 ion could be formed by further scission of a shorter fragment ion e.g.

(ii) [CH₃CH₂CH₂CH₂CH₂]⁺ ===> [CH₃CH₂CH₂CH₂]⁺ + CH₂

The m/z 58 ion is probably formed in the same way but contains a ¹³C atom i.e. it has the formula [¹³C¹²C₃H₉]⁺ rather than [C₄H₁₀]⁺

Note that an accurate mass spectrometer can sort out (resolve) pairs of ions with the same integer m/z value because they can measure relative fragment ion masses to four decimal places,

e.g. using accurate relative isotopic masses:

¹H = 1.0078 ¹²C = 12.0000 ¹³C = 13.0034: you can then calculate (predict) that the accurate relative ion masses are:

For m/z 58: [¹³C¹²C₃H₉]⁺ = 58.0736, [C₄H₁₀]⁺ = 58.0780, a difference of 0.0044 in relative ion mass.

Formation of m/z 43 ion:

[CH₃CH₂CH₂CH₂CH₂CH₃]⁺ ===> [CH₃CH₂CH₂]⁺ + CH₂CH₂CH₃

C-C bond scission of the parent molecular ion, loss of propyl group,

mass change = 86 - 43 = 43 (M-43 ion peak)

The m/z 44 ion is probably formed in the same way but contains a ¹³C atom i.e. it has the formula [¹³C¹²C₂H₇]⁺ rather than [C₃H₈]⁺

So again, using accurate relative isotopic masses:

¹H = 1.0078 ¹²C = 12.0000 ¹³C = 13.0034: you can then calculate (predict) that the accurate relative ion masses are:

For m/z 44: [C₃H₈]⁺ = 44.0624 and [¹³C¹²C₂H₇]⁺ = 44.0580, a difference of 0.0044 in relative ion mass.

Formation of m/z 29 ion:

[CH₃CH₂CH₂CH₂CH₂CH₃]⁺ ===> [CH₃CH₂]⁺ + CH₂CH₂CH₂CH₃

C-C bond scission of the parent molecular ion, loss of butyl group,

mass change = 86 - 57 = 29 (M-57 ion peak)

Sequences including m/z values of 42, 41, 40, 39 or 28, 28, 27, 26, indicate successive hydrogen atom/molecule loss from the m/z 43 or 29 ions.

Comparing the infrared, mass, 1H NMR and 13C NMR spectra of the five structural alkane isomers of C₆H₁₄ NOTE: The images are linked to their original detailed spectral analysis pages AND can be doubled in size with touch screens to increase the definition to the original hexane, 2-methylpentane, 3-methylpentane, 2,2-dimethylbutane and 2,3-dimethylbutane image sizes. These five molecules are structural isomers of saturated alkanes of molecular formula C₆H₁₄ and exemplify the infrared, mass, ¹H NMR and ¹³C NMR spectra of lower aliphatic alkanes (non-cyclic alkanes).
Infrared spectra below.

	INFRARED SPECTRA: Apart from the significant differences in the fingerprint region at wavenumbers 1500 to 400 cm^-1, there are no other great striking differences, but each could be identified from its infrared spectrum. All the absorption bands are typical of molecules containing saturated alkyl structure and there are no characteristic infrared absorptions due to a specific functional group.

Infrared spectra above, mass spectra below.

	MASS SPECTRA: Base ion peaks plus m/z comments. Hexane: m/z 57, 42 and 56 prominent 2-methylpentane: m/z 43, 42 and 71 prominent 3-methylpentane: m/z 57, 41 and 56 prominent 2,2-dimethylbutane: m/z 43, 41, 57 and 71 prominent 2,3-dimethylbutane: m/z 43, 41, 42 and 71 prominent

Mass spectra above, 1H NMR spectra below.

	1H NMR SPECTRA: They can all be distinguished by their different integrated proton ratios - need very high resolution. Hexane: 3 ¹H δ shifts, H ratio 3:2:2 (6:4:4 in formula) 2-methylpentane: 5 ¹H δ shifts, H ratio 6:3:2:2:1 3-methylpentane: 4 ¹H δ shifts, H ratio 6:4:3:1 2,2-dimethylbutane: 3 ¹H δ shifts, H ratio 9:3:2 2,3-dimethylbutane: 2 ¹H δ shifts, H ratio 6:1 (12:2 in formula)

1H NMR spectra above, 13C NMR spectra below.

	13C NMR SPECTRA: From the number of shifts, you can't distinguish (iii) and (iv) but you can distinguish them from (i), (ii) and (v). (i) Hexane: 3 ¹³C δ shifts (ii) 2-methylpentane: 5 ¹³C δ shifts (iii) 3-methylpentane: 4 ¹³C δ shifts (iv) 2,2-dimethylbutane: 4 ¹³C δ shifts (v) 2,3-dimethylbutane: 2 ¹³C δ shifts

13C NMR spectra above.

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The H-1 NMR spectrum of hexane

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